function gapfilledGenomeAnnotation = gapfillRefinedGenomeReactions(genomeAnnotation)
% Part of the DEMETER pipelinbe. Adds reactions needed to connect pathways 
% introduced based on comparative genomic analyses.comparative genomics.
%
% USAGE:
%   gapfilledGenomeAnnotation = gapfillRefinedGenomeReactions(genomeAnnotation)
%
% INPUT
% genomeAnnotation              Text file with genome annotations that had 
%                               been retrieved through the function
%                               writeReactionsFromPubSeedSpreadsheets
% OUTPUT
% gapfilledGenomeAnnotation     Text file with genome annotations that have
%                               been gap-filled to enable flux through 
%                               reactions added based on genome annotations
%
% .. Author:
%       - Almut Heinken, 06/2020

replaceRxns={'7BHGLZabc','7BHGLZGLCabc';'1HIBUP_Sabc','1HIBUPGLU_Sabc';'2HIBUP_Sabc','2HIBUPGLU_Sabc';'3HIBUP_Sabc','3HIBUPGLU_Sabc';'CARIBUP_Sabc','CARIBUPGLU_Sabc';'5OH_SP_GLCabc','5OH_SULFP_GLCabc';'1HIBUP_St','1HIBUPGLU_St';'2HIBUP_St','2HIBUPGLU_St';'3HIBUP_St','3HIBUPGLU_St';'5OH_SP_GLCt','5OH_SULFP_GLCt';'7BHGLZt','7BHGLZGLCt';'CARIBUP_St','CARIBUPGLU_St';'1HIBUP_St2','1HIBUPGLU_St2';'2HIBUP_St2','2HIBUPGLU_St2';'3HIBUP_St2','3HIBUPGLU_St2';'7BHGLZGLCte','7BHGLZte';'1HIBUPGLU_Ste','1HIBUP_Ste';'2HIBUPGLU_Ste','2HIBUP_Ste';'3HIBUPGLU_Ste','3HIBUP_Ste';'CARIBUPGLU_Ste','CARIBUP_Ste';'5OH_SPte','5OH_SULFPte';'7BHGLZt2','7BHGLZGLCt2';'CARIBUP_St2','CARIBUPGLU_St2';'5OH_SP_GLCt2','5OH_SULFP_GLCt2';'EX_5oh_sp(e)','EX_5oh_sulfp(e)';'EX_5oh_sp_glc(e)','EX_5oh_sulfp_glc(e)';'5OH_SPte','5OH_SULFPte';'56DFURP','DH5FURAt';'DM_na1(c)','DM_NA1'};

for i=1:length(replaceRxns)
    genomeAnnotation(:,2)=strrep(genomeAnnotation(:,2),replaceRxns{i,1},replaceRxns{i,2});
end

% Define reaction-specific gapfills
gapfills={
    'Present','Absent','GapfillRxns'
    {'CZP_NR'},{'tCZP'}, {'tCZP','tNZP','tNZP','EX_czp(e)','EX_nzp(e)','tCAP','tNCAP','EX_chlphncl(e)','EX_nchlphncl(e)','t7ACZP','tANZP','EX_7a_czp(e)','EX_anzp(e)'}
    {'PTVSTGLUC_GLCAASEe'},{'EX_ptvst(e)'}, {'EX_ptvst(e)'}
    {'4HPHACDC'},{'HPACt2r'}, {'EX_4hphac(e)', 'HPACt2r', 'EX_pcresol(e)', 'PCRESOLt2r'}
    {'5FURADH'},{'DH5FURAt'}, {'EX_dh5fura(e)', 'DH5FURAt', 'EX_5fura(e)', '5FURAt'}
    {'56DFURADH'},{'DH5FURAt'}, {'EX_dh5fura(e)', 'DH5FURAt', 'EX_5fura(e)', '5FURAt'}
    {'DFDCYTDD'},{'DFDCYTDabc'}, {'EX_dfdcytd(e)', 'DFDCYTDabc'}
    {'DFDCYTDD'},{'DFDURIte'}, {'EX_dfduri(e)', 'DFDURIte'}
    {'AC5ASAc'},{'AC5ASAp'}, {'EX_ac5asa(e)', 'AC5ASAp'}
    {'AC5ASAc'},{'5ASAp','5ASAt2r'}, {'EX_5asa(e)', '5ASAp'}
    {'ISNZDAc'},{'ISNZDp'}, {'EX_isnzd(e)', 'ISNZDp'}
    {'ISNZDAc'},{'ACISNZDp'}, {'EX_acisnzd(e)', 'ACISNZDp'}
    {'BZD_AR_NAD'},{'5ASAp','5ASAt2r'}, {'5ASAt2r'}
    {'BZD_AR_NADP'},{'5ASAp','5ASAt2r'}, {'5ASAt2r'}
    {'ALKP_R788'}, {'R788t2'}, {'R788t2', 'EX_r788(e)', 'EX_r406(e)', 'R406te'}
    {'BZD_AR_NAD'},{'BZDt2r'}, {'BZDt2r','NEOPRONTt2r','OLSAt2r','PRONTt2r','SSZt2r','ABZ_ALA_Bt2r', 'SANILAMIDEt2r', 'SULFPt2r', 'TABt2r'}
    {'BZD_AR_NAD'},{'EX_bzd(e)'}, {'EX_bzd(e)','EX_abz_ala_b(e)','EX_5asa(e)','EX_olsa(e)','EX_neopront(e)','EX_sanilamide(e)','EX_ssz(e)','EX_sulfp(e)','EX_tab(e)','EX_pront(e)'}
    {'BZD_AR_NADP'},{'BZDt2r'}, {'BZDt2r','NEOPRONTt2r','OLSAt2r','PRONTt2r','SSZt2r','ABZ_ALA_Bt2r', 'SANILAMIDEt2r', 'SULFPt2r', 'TABt2r'}
    {'BZD_AR_NADP'},{'EX_bzd(e)'}, {'EX_bzd(e)','EX_abz_ala_b(e)','EX_5asa(e)','EX_olsa(e)','EX_neopront(e)','EX_sanilamide(e)','EX_ssz(e)','EX_sulfp(e)','EX_tab(e)','EX_pront(e)'}
    {'FCSND'},{'FCSNt'}, {'EX_fcsn(e)', 'FCSNt'}
    {'FCSND'},{'5FURAt'}, {'EX_5fura(e)', '5FURAt'}
    {'1HIBUP_S_GLCAASE'},{'1HIBUP_Ste'}, {'1HIBUP_Ste','1OHMDZte','2HATVACIDte','2HATVLACte','2HIBUP_Ste','2OH_CBZte','2OH_MTZte','3HIBUP_Ste','3MEACMPte','3OH_CBZte','3OH_DLORte','3OH_MDEAte','3OH_MXNte','4DH_TPNOte','4OH_DCFte','4OH_KPte','4OH_LEVOLEte','4OH_METHte','4OH_PROPLte','4OH_TRZte','4OH_VCZte','4OHMDZte','5OH_SULFPte','5OHFVSte','6BHGLZte','6OHFVSte','7BHGLZte','7OH_EFVte','814DIOH_EFVte','8OH_EFVte','AC_AMN_B_GLYte','ACMPte','ALPZ_4OHte','ALPZ_AOHte','AM14te','AM1CCSte','AM5te','AM6te','AMIOte','AMIO_Cte','AMN_B_GLYte','AMNTD_M6te','ATVACIDte','ATVLACte','BHPMte','BILR_355te','BILR_M14te','BILR_M7te','BSNte','BZte','CARIBUP_Ste','CBZte','CD6168te','CHLPHNCLte','CLCXBte','CLCXB_Cte','CLOBI_Cte','CRVSM1te','CRVSM23te','DAAte','DCFte','DDEAte','DES_ASTZLte','DIGOXINte','DLBte','DNPZ_5DESte','DNPZ_6DESte','DNPZ_M9te','DOH_ETRte','DOH_VCZte','DXOte','EFVte','ELTRte','EZTMBte','FVSte','FVSTETte','GLTMNte','GMFLte','GMFL_MIte','GMFL_MIIte','GMFL_MIIIte','HSTte','HST_3_GLCte','HST_3_Ste','HST_7_GLCte','HST_7_Ste','IBUP_Ste','IMNte','INVte','ISOSORBIDE_5MNte','KPROFENte','LST4EXPte','LSTNte','MDZte','MISOte','MRPHNte','MTZte','N_OH_PHTNte','NSLDP_M5te','NVERPte','ODSM_EGLTMNte','ODSM_GLTMNte','OH_ETRte','OH_PBLte','PHPPAte','PROBte','PRONTte','PROPLte','PRX_MIte','PRX_MIIte','PTVSTte','PVSte','R_6OH_WARFte','R_7OH_WARFte','R_8OH_WARFte','R406te','R529te','REPte','RPN_104557te','RPN_96990te','RPN_OHte','RSVte','S_4OH_WARFte','S_6OH_WARFte','SB_611855te','SB_Yte','SCH_57871te','SFND_1689te','SFTZte','SMAPte','SMVACIDte','SN38te','SPZte','SPZ_SFNte','STGte','TGZte','THSACMPte','TLF_A_1Ate','TLF_A_1Bte','TLF_A_1Xte','TLF_A_2te','TLF_A_2Ate','TLF_A_3te','TLF_A_4te','TLF_A_M5te','TLMSte','TMACMPte','TOLCPte','TOLCP_ACte','TOLCP_AMte','TPNO_4Gte','TPNOHte','TLF_Ate','ESTRONEt','ESTRADIOLte','ESTRIOLte','REGFNBte'}
    {'1HIBUP_S_GLCAASE'},{'1HIBUPGLU_Sabc','1HIBUPGLU_St2','1HIBUPGLU_St'}, {'1HIBUPGLU_St2','1HIBUPGLU_St2','1HMDGLUCt2','2HATVACIDGLUCt2','2HATVLACGLUCt2','2HIBUPGLU_St2','2HIBUPGLU_St2','2OH_CBZ_GLCt2','2OH_MTZ_GLCt2','3HIBUPGLU_St2','3HIBUPGLU_St2','3OH_CBZ_GLCt2','3OH_DLOR_GLCt2','3OH_MDEA_GLCt2','3OH_MXN_GLCt2','4DH_TPNO_1GLCt2','4HMDGLUCt2','4OH_DCF_GLCt2','4OH_KP_GLCt2','4OH_LEVOLE_GLCt2','4OH_METH_GLCt2','4OH_PROPL_GLCt2','4OH_TRZ_GLCt2','4OH_VCZ_GLCt2','5OH_SULFP_GLCt2','5OHFVSGLUt2','6BHGLZGLCt2','6OHFVSGLUt2','7BHGLZGLCt2','7OH_EFV_GLCt2','814DIOH_EFV_GLCt2','8OH_EFV_GLCt2','AC_AMN_B_GLY_GLCt2','ACMP_GLCt2','ACMPGLUt2','ALPZ_4OH_GLCt2','ALPZ_AOH_GLCt2','AM14_GLCt2','AM1CGLCt2','AM5_GLCt2','AM6_GLCt2','AMIO_C_GLCt2','AMIO_GLCt2','AMN_B_GLY_GLCt2','AMNTD_M6_GLCt2','ATVACYLGLUCt2','ATVETHGLUCt2','ATVLACGLUCt2','BHPM_GLCt2','BILR_M10t2','BILR_M12t2','BILR_M15t2','BILR_M16t2','BSN_GLCt2','BZ_GLCt2','CARIBUPGLU_St2','CBZ_GLCt2','CD6168_GLCt2','CHLPHNCL_GLCt2','CLCXB_C_GLCt2','CLCXB_GLCt2','CLOBI_GLCt2','CVM1GLUCt2','CVM23GLUCt2','DAA_GLCt2','DCF_GLCt2','DDEA_GLCt2','DES_ASTZL_GLCt2','DIGOXIN_GLCt2','DLB_GLCt2','DNPZ_M11t2','DNPZ_M12t2','DNPZ_M13t2','DNPZ_M14t2','DOH_ETR_GLCt2','DOH_VCZ_GLCt2','DXO_GLCt2','EFV_GLCt2','ELTR_GLCt2','ELTR_M3t2','ELTR_M4t2','EZTMB_GLCt2','FVSGLUCt2','FVSTETGLUt2','GLC3MEACPt2','GLTMN_GLCt2','GMFL_GLCt2','GMFL_MI_GLCt2','GMFL_MII_GLCt2','GMFL_MIII_GLCt2','GTACMPt2','HST_3_GLCt2','HST_37_DIGLCt2','HST_3GLC_7St2','HST_7_GLCt2','HST_7GLC_3St2','IBUPGLUCt2','IMN_GLCt2','INV_M1t2','ISOSORBIDE_5MN_GLCt2','KPROFEN_GLCt2','LSTN1GLUCt2','LSTNM4t2','LSTNM7t2','MDZ_GLCt2','MDZGLCt2','MISO_GLCt2','MRPHN_3GLCt2','MRPHN_6GLCt2','MTZ_GLCt2','N_OH_PHTN_GLCt2','NSLDP_M5_GLCt2','NVERP_GLCt2','ODSM_EGLTMN_GLCt2','ODSM_GLTMN_GLCt2','OH_ETR_GLCt2','OH_PBL_GLCt2','PHPPA_GLCt2','PHTN_GLCt2','PROB_GLCt2','PRONT_GLCt2','PROPL_GLCt2','PRX_MI_GLCt2','PRX_MII_GLCt2','PTVSTGLUCt2','PVSGLUCt2','R_6OH_WARF_GLCt2','R_7OH_WARF_GLCt2','R_8OH_WARF_GLCt2','R406_GLCt2','R529_GLCt2','REP_GLCt2','RPN_104557_CB_GLCt2','RPN_96990_GLCt2','RPN_OH_GLCt2','RSVGLUCt2','S_4OH_WARF_GLCt2','S_6OH_WARF_GLCt2','SCH_488128t2','SCH_57871_GLCt2','SFND_1689_GLCt2','SFTZ_GLCt2','SIMVGLUCt2','SMAP_GLCt2','SN38Gt2','SPZ_GLCt2','SPZ_SFN_GLCt2','STG_M3t2','STG_M4t2','TATt2','TGZ_GLCt2','TLF_A_M1t2','TLF_A_M2t2','TLF_A_M3t2','TLF_A_M4At2','TLF_A_M4t2','TLF_A_M5At2','TLF_A_M5Bt2','TLF_A_M5t2','TLF_A_M6t2','TLF_A_M9t2','TLMS_GLCt2','TOLCP_AC_GLCt2','TOLCP_AM_GLCt2','TOLCP_GLCt2','TPNO_1GLC_4Gt2','TPNO_4GLCt2','TSACMGLUCt2'}
    {'1HIBUP_S_GLCAASE'},{'EX_1hibup_S(e)'}, {'EX_1hibup_S(e)','EX_1hibupglu_S(e)','EX_1hmdgluc(e)','EX_1ohmdz(e)','EX_2hatvacid(e)','EX_2hatvacidgluc(e)','EX_2hatvlac(e)','EX_2hatvlacgluc(e)','EX_2hibup_S(e)','EX_2hibupglu_S(e)','EX_2oh_cbz(e)','EX_2oh_cbz_glc(e)','EX_2oh_mtz(e)','EX_2oh_mtz_glc(e)','EX_3meacmp(e)','EX_3hibup_S(e)','EX_3hibupglu_S(e)','EX_3oh_cbz(e)','EX_3oh_cbz_glc(e)','EX_3oh_dlor(e)','EX_3oh_dlor_glc(e)','EX_3oh_mdea(e)','EX_3oh_mdea_glc(e)','EX_3oh_mxn(e)','EX_3oh_mxn_glc(e)','EX_4dh_tpno(e)','EX_4dh_tpno_1glc(e)','EX_4hmdgluc(e)','EX_4oh_dcf(e)','EX_4oh_dcf_glc(e)','EX_4oh_kp(e)','EX_4oh_kp_glc(e)','EX_4oh_levole(e)','EX_4oh_levole_glc(e)','EX_4oh_meth(e)','EX_4oh_meth_glc(e)','EX_4oh_propl(e)','EX_4oh_propl_glc(e)','EX_4oh_trz(e)','EX_4oh_trz_glc(e)','EX_4oh_vcz(e)','EX_4oh_vcz_glc(e)','EX_4ohmdz(e)','EX_5oh_sulfp(e)','EX_5oh_sulfp_glc(e)','EX_5ohfvs(e)','EX_5ohfvsglu(e)','EX_6bhglz(e)','EX_6bhglzglc(e)','EX_6ohfvs(e)','EX_6ohfvsglu(e)','EX_7bhglz(e)','EX_7bhglzglc(e)','EX_7oh_efv(e)','EX_7oh_efv_glc(e)','EX_814dioh_efv(e)','EX_814dioh_efv_glc(e)','EX_8oh_efv(e)','EX_8oh_efv_glc(e)','EX_ac_amn_b_gly(e)','EX_ac_amn_b_gly_glc(e)','EX_acmp(e)','EX_acmp_glc(e)','EX_acmpglu(e)','EX_alpz_4oh(e)','EX_alpz_4oh_glc(e)','EX_alpz_aoh(e)','EX_alpz_aoh_glc(e)','EX_am14(e)','EX_am14_glc(e)','EX_am1ccs(e)','EX_am1cglc(e)','EX_am5(e)','EX_am5_glc(e)','EX_am6(e)','EX_am6_glc(e)','EX_amio(e)','EX_amio_c(e)','EX_amio_c_glc(e)','EX_amio_glc(e)','EX_amn_b_gly(e)','EX_amn_b_gly_glc(e)','EX_amntd_m6(e)','EX_amntd_m6_glc(e)','EX_atvacid(e)','EX_atvacylgluc(e)','EX_atvethgluc(e)','EX_atvlac(e)','EX_atvlacgluc(e)','EX_bhpm(e)','EX_bhpm_glc(e)','EX_bilr_355(e)','EX_bilr_M10(e)','EX_bilr_M12(e)','EX_bilr_M14(e)','EX_bilr_M15(e)','EX_bilr_M16(e)','EX_bilr_M7(e)','EX_bsn(e)','EX_bsn_glc(e)','EX_bz(e)','EX_bz_glc(e)','EX_caribup_s(e)','EX_caribupglu_S(e)','EX_cbz(e)','EX_cbz_glc(e)','EX_cd6168(e)','EX_cd6168_glc(e)','EX_chlphncl(e)','EX_chlphncl_glc(e)','EX_clcxb(e)','EX_clcxb_c(e)','EX_clcxb_c_glc(e)','EX_clcxb_glc(e)','EX_clobi_c(e)','EX_clobi_glc(e)','EX_crvsm1(e)','EX_crvsm23(e)','EX_cvm1gluc(e)','EX_cvm23gluc(e)','EX_daa(e)','EX_daa_glc(e)','EX_dcf(e)','EX_dcf_glc(e)','EX_ddea(e)','EX_ddea_glc(e)','EX_des_astzl(e)','EX_des_astzl_glc(e)','EX_digoxin(e)','EX_digoxin_glc(e)','EX_dlb(e)','EX_dlb_glc(e)','EX_dnpz_5des(e)','EX_dnpz_6des(e)','EX_dnpz_m11(e)','EX_dnpz_m12(e)','EX_dnpz_m13(e)','EX_dnpz_m14(e)','EX_dnpz_m9(e)','EX_doh_etr(e)','EX_doh_etr_glc(e)','EX_doh_vcz(e)','EX_doh_vcz_glc(e)','EX_dxo(e)','EX_dxo_glc(e)','EX_efv(e)','EX_efv_glc(e)','EX_eltr(e)','EX_eltr_glc(e)','EX_eltr_m3(e)','EX_eltr_m4(e)','EX_eztmb(e)','EX_eztmb_glc(e)','EX_fvs(e)','EX_fvsgluc(e)','EX_fvstet(e)','EX_fvstetglu(e)','EX_glc3meacp(e)','EX_gltmn(e)','EX_gltmn_glc(e)','EX_gmfl(e)','EX_gmfl_glc(e)','EX_gmfl_mI(e)','EX_gmfl_mI_glc(e)','EX_gmfl_mII(e)','EX_gmfl_mII_glc(e)','EX_gmfl_mIII(e)','EX_gmfl_mIII_glc(e)','EX_gtacmp(e)','EX_hst(e)','EX_hst_3_glc(e)','EX_hst_3_s(e)','EX_hst_37_diglc(e)','EX_hst_3glc_7s(e)','EX_hst_7_glc(e)','EX_hst_7_s(e)','EX_hst_7glc_3s(e)','EX_ibup_S(e)','EX_ibupgluc(e)','EX_imn(e)','EX_imn_glc(e)','EX_inv(e)','EX_inv_m1(e)','EX_isosorbide_5mn(e)','EX_isosorbide_5mn_glc(e)','EX_kprofen(e)','EX_kprofen_glc(e)','EX_lst4exp(e)','EX_lstn(e)','EX_lstn1gluc(e)','EX_lstnm4(e)','EX_lstnm7(e)','EX_mdz(e)','EX_mdz_glc(e)','EX_mdzglc(e)','EX_miso(e)','EX_miso_glc(e)','EX_mrphn(e)','EX_mrphn_3glc(e)','EX_mrphn_6glc(e)','EX_mtz(e)','EX_mtz_glc(e)','EX_N_oh_phtn(e)','EX_N_oh_phtn_glc(e)','EX_nsldp_m5(e)','EX_nsldp_m5_glc(e)','EX_nverp(e)','EX_nverp_glc(e)','EX_odsm_egltmn(e)','EX_odsm_egltmn_glc(e)','EX_odsm_gltmn(e)','EX_odsm_gltmn_glc(e)','EX_oh_etr(e)','EX_oh_etr_glc(e)','EX_oh_pbl(e)','EX_oh_pbl_glc(e)','EX_phppa(e)','EX_phppa_glc(e)','EX_phtn_glc(e)','EX_prob(e)','EX_prob_glc(e)','EX_pront(e)','EX_pront_glc(e)','EX_propl(e)','EX_propl_glc(e)','EX_prx_mI(e)','EX_prx_mI_glc(e)','EX_prx_mII(e)','EX_prx_mII_glc(e)','EX_ptvst(e)','EX_ptvstgluc(e)','EX_pvs(e)','EX_pvsgluc(e)','EX_R_6oh_warf(e)','EX_R_6oh_warf_glc(e)','EX_R_7oh_warf(e)','EX_R_7oh_warf_glc(e)','EX_R_8oh_warf(e)','EX_R_8oh_warf_glc(e)','EX_r406(e)','EX_r406_glc(e)','EX_r529(e)','EX_r529_glc(e)','EX_rep(e)','EX_rep_glc(e)','EX_rpn_104557(e)','EX_rpn_104557_cb_glc(e)','EX_rpn_96990(e)','EX_rpn_96990_glc(e)','EX_rpn_oh(e)','EX_rpn_oh_glc(e)','EX_rsv(e)','EX_rsvgluc(e)','EX_S_4oh_warf(e)','EX_S_4oh_warf_glc(e)','EX_S_6oh_warf(e)','EX_S_6oh_warf_glc(e)','EX_sb_611855(e)','EX_sb_y(e)','EX_sch_488128(e)','EX_sch_57871(e)','EX_sch_57871_glc(e)','EX_sfnd_1689(e)','EX_sfnd_1689_glc(e)','EX_sftz(e)','EX_sftz_glc(e)','EX_simvgluc(e)','EX_smap(e)','EX_smap_glc(e)','EX_smvacid(e)','EX_sn38(e)','EX_sn38g(e)','EX_spz(e)','EX_spz_glc(e)','EX_spz_sfn(e)','EX_spz_sfn_glc(e)','EX_stg(e)','EX_stg_m3(e)','EX_stg_m4(e)','EX_tat(e)','EX_tgz(e)','EX_tgz_glc(e)','EX_thsacmp(e)','EX_tlf_a(e)','EX_tlf_a_1a(e)','EX_tlf_a_1b(e)','EX_tlf_a_1x(e)','EX_tlf_a_2(e)','EX_tlf_a_2a(e)','EX_tlf_a_3(e)','EX_tlf_a_4(e)','EX_tlf_a_m1(e)','EX_tlf_a_m2(e)','EX_tlf_a_m3(e)','EX_tlf_a_m4(e)','EX_tlf_a_m4a(e)','EX_tlf_a_m5(e)','EX_tlf_a_m5a(e)','EX_tlf_a_m5b(e)','EX_tlf_a_m6(e)','EX_tlf_a_m9(e)','EX_tlms(e)','EX_tlms_glc(e)','EX_tmacmp(e)','EX_tolcp(e)','EX_tolcp_ac(e)','EX_tolcp_ac_glc(e)','EX_tolcp_am(e)','EX_tolcp_am_glc(e)','EX_tolcp_glc(e)','EX_tpno_1glc_4g(e)','EX_tpno_4g(e)','EX_tpno_4glc(e)','EX_tpnoh(e)','EX_tsacmgluc(e)','EX_estroneglc(e)','EX_estrone(e)','EX_estradiolglc(e)','EX_estradiol(e)','EX_estriolglc(e)','EX_estriol(e)','EX_regfnb_glc(e)','EX_regfnb(e)'}
    {'1HIBUP_S_GLCAASEe'},{'EX_1hibup_S(e)'}, {'EX_1hibup_S(e)','EX_1hibupglu_S(e)','EX_1hmdgluc(e)','EX_1ohmdz(e)','EX_2hatvacid(e)','EX_2hatvacidgluc(e)','EX_2hatvlac(e)','EX_2hatvlacgluc(e)','EX_2hibup_S(e)','EX_2hibupglu_S(e)','EX_2oh_cbz(e)','EX_2oh_cbz_glc(e)','EX_2oh_mtz(e)','EX_2oh_mtz_glc(e)','EX_3meacmp(e)','EX_3hibup_S(e)','EX_3hibupglu_S(e)','EX_3oh_cbz(e)','EX_3oh_cbz_glc(e)','EX_3oh_dlor(e)','EX_3oh_dlor_glc(e)','EX_3oh_mdea(e)','EX_3oh_mdea_glc(e)','EX_3oh_mxn(e)','EX_3oh_mxn_glc(e)','EX_4dh_tpno(e)','EX_4dh_tpno_1glc(e)','EX_4hmdgluc(e)','EX_4oh_dcf(e)','EX_4oh_dcf_glc(e)','EX_4oh_kp(e)','EX_4oh_kp_glc(e)','EX_4oh_levole(e)','EX_4oh_levole_glc(e)','EX_4oh_meth(e)','EX_4oh_meth_glc(e)','EX_4oh_propl(e)','EX_4oh_propl_glc(e)','EX_4oh_trz(e)','EX_4oh_trz_glc(e)','EX_4oh_vcz(e)','EX_4oh_vcz_glc(e)','EX_4ohmdz(e)','EX_5oh_sulfp(e)','EX_5oh_sulfp_glc(e)','EX_5ohfvs(e)','EX_5ohfvsglu(e)','EX_6bhglz(e)','EX_6bhglzglc(e)','EX_6ohfvs(e)','EX_6ohfvsglu(e)','EX_7bhglz(e)','EX_7bhglzglc(e)','EX_7oh_efv(e)','EX_7oh_efv_glc(e)','EX_814dioh_efv(e)','EX_814dioh_efv_glc(e)','EX_8oh_efv(e)','EX_8oh_efv_glc(e)','EX_ac_amn_b_gly(e)','EX_ac_amn_b_gly_glc(e)','EX_acmp(e)','EX_acmp_glc(e)','EX_acmpglu(e)','EX_alpz_4oh(e)','EX_alpz_4oh_glc(e)','EX_alpz_aoh(e)','EX_alpz_aoh_glc(e)','EX_am14(e)','EX_am14_glc(e)','EX_am1ccs(e)','EX_am1cglc(e)','EX_am5(e)','EX_am5_glc(e)','EX_am6(e)','EX_am6_glc(e)','EX_amio(e)','EX_amio_c(e)','EX_amio_c_glc(e)','EX_amio_glc(e)','EX_amn_b_gly(e)','EX_amn_b_gly_glc(e)','EX_amntd_m6(e)','EX_amntd_m6_glc(e)','EX_atvacid(e)','EX_atvacylgluc(e)','EX_atvethgluc(e)','EX_atvlac(e)','EX_atvlacgluc(e)','EX_bhpm(e)','EX_bhpm_glc(e)','EX_bilr_355(e)','EX_bilr_M10(e)','EX_bilr_M12(e)','EX_bilr_M14(e)','EX_bilr_M15(e)','EX_bilr_M16(e)','EX_bilr_M7(e)','EX_bsn(e)','EX_bsn_glc(e)','EX_bz(e)','EX_bz_glc(e)','EX_caribup_s(e)','EX_caribupglu_S(e)','EX_cbz(e)','EX_cbz_glc(e)','EX_cd6168(e)','EX_cd6168_glc(e)','EX_chlphncl(e)','EX_chlphncl_glc(e)','EX_clcxb(e)','EX_clcxb_c(e)','EX_clcxb_c_glc(e)','EX_clcxb_glc(e)','EX_clobi_c(e)','EX_clobi_glc(e)','EX_crvsm1(e)','EX_crvsm23(e)','EX_cvm1gluc(e)','EX_cvm23gluc(e)','EX_daa(e)','EX_daa_glc(e)','EX_dcf(e)','EX_dcf_glc(e)','EX_ddea(e)','EX_ddea_glc(e)','EX_des_astzl(e)','EX_des_astzl_glc(e)','EX_digoxin(e)','EX_digoxin_glc(e)','EX_dlb(e)','EX_dlb_glc(e)','EX_dnpz_5des(e)','EX_dnpz_6des(e)','EX_dnpz_m11(e)','EX_dnpz_m12(e)','EX_dnpz_m13(e)','EX_dnpz_m14(e)','EX_dnpz_m9(e)','EX_doh_etr(e)','EX_doh_etr_glc(e)','EX_doh_vcz(e)','EX_doh_vcz_glc(e)','EX_dxo(e)','EX_dxo_glc(e)','EX_efv(e)','EX_efv_glc(e)','EX_eltr(e)','EX_eltr_glc(e)','EX_eltr_m3(e)','EX_eltr_m4(e)','EX_eztmb(e)','EX_eztmb_glc(e)','EX_fvs(e)','EX_fvsgluc(e)','EX_fvstet(e)','EX_fvstetglu(e)','EX_glc3meacp(e)','EX_gltmn(e)','EX_gltmn_glc(e)','EX_gmfl(e)','EX_gmfl_glc(e)','EX_gmfl_mI(e)','EX_gmfl_mI_glc(e)','EX_gmfl_mII(e)','EX_gmfl_mII_glc(e)','EX_gmfl_mIII(e)','EX_gmfl_mIII_glc(e)','EX_gtacmp(e)','EX_hst(e)','EX_hst_3_glc(e)','EX_hst_3_s(e)','EX_hst_37_diglc(e)','EX_hst_3glc_7s(e)','EX_hst_7_glc(e)','EX_hst_7_s(e)','EX_hst_7glc_3s(e)','EX_ibup_S(e)','EX_ibupgluc(e)','EX_imn(e)','EX_imn_glc(e)','EX_inv(e)','EX_inv_m1(e)','EX_isosorbide_5mn(e)','EX_isosorbide_5mn_glc(e)','EX_kprofen(e)','EX_kprofen_glc(e)','EX_lst4exp(e)','EX_lstn(e)','EX_lstn1gluc(e)','EX_lstnm4(e)','EX_lstnm7(e)','EX_mdz(e)','EX_mdz_glc(e)','EX_mdzglc(e)','EX_miso(e)','EX_miso_glc(e)','EX_mrphn(e)','EX_mrphn_3glc(e)','EX_mrphn_6glc(e)','EX_mtz(e)','EX_mtz_glc(e)','EX_N_oh_phtn(e)','EX_N_oh_phtn_glc(e)','EX_nsldp_m5(e)','EX_nsldp_m5_glc(e)','EX_nverp(e)','EX_nverp_glc(e)','EX_odsm_egltmn(e)','EX_odsm_egltmn_glc(e)','EX_odsm_gltmn(e)','EX_odsm_gltmn_glc(e)','EX_oh_etr(e)','EX_oh_etr_glc(e)','EX_oh_pbl(e)','EX_oh_pbl_glc(e)','EX_phppa(e)','EX_phppa_glc(e)','EX_phtn_glc(e)','EX_prob(e)','EX_prob_glc(e)','EX_pront(e)','EX_pront_glc(e)','EX_propl(e)','EX_propl_glc(e)','EX_prx_mI(e)','EX_prx_mI_glc(e)','EX_prx_mII(e)','EX_prx_mII_glc(e)','EX_ptvst(e)','EX_ptvstgluc(e)','EX_pvs(e)','EX_pvsgluc(e)','EX_R_6oh_warf(e)','EX_R_6oh_warf_glc(e)','EX_R_7oh_warf(e)','EX_R_7oh_warf_glc(e)','EX_R_8oh_warf(e)','EX_R_8oh_warf_glc(e)','EX_r406(e)','EX_r406_glc(e)','EX_r529(e)','EX_r529_glc(e)','EX_rep(e)','EX_rep_glc(e)','EX_rpn_104557(e)','EX_rpn_104557_cb_glc(e)','EX_rpn_96990(e)','EX_rpn_96990_glc(e)','EX_rpn_oh(e)','EX_rpn_oh_glc(e)','EX_rsv(e)','EX_rsvgluc(e)','EX_S_4oh_warf(e)','EX_S_4oh_warf_glc(e)','EX_S_6oh_warf(e)','EX_S_6oh_warf_glc(e)','EX_sb_611855(e)','EX_sb_y(e)','EX_sch_488128(e)','EX_sch_57871(e)','EX_sch_57871_glc(e)','EX_sfnd_1689(e)','EX_sfnd_1689_glc(e)','EX_sftz(e)','EX_sftz_glc(e)','EX_simvgluc(e)','EX_smap(e)','EX_smap_glc(e)','EX_smvacid(e)','EX_sn38(e)','EX_sn38g(e)','EX_spz(e)','EX_spz_glc(e)','EX_spz_sfn(e)','EX_spz_sfn_glc(e)','EX_stg(e)','EX_stg_m3(e)','EX_stg_m4(e)','EX_tat(e)','EX_tgz(e)','EX_tgz_glc(e)','EX_thsacmp(e)','EX_tlf_a(e)','EX_tlf_a_1a(e)','EX_tlf_a_1b(e)','EX_tlf_a_1x(e)','EX_tlf_a_2(e)','EX_tlf_a_2a(e)','EX_tlf_a_3(e)','EX_tlf_a_4(e)','EX_tlf_a_m1(e)','EX_tlf_a_m2(e)','EX_tlf_a_m3(e)','EX_tlf_a_m4(e)','EX_tlf_a_m4a(e)','EX_tlf_a_m5(e)','EX_tlf_a_m5a(e)','EX_tlf_a_m5b(e)','EX_tlf_a_m6(e)','EX_tlf_a_m9(e)','EX_tlms(e)','EX_tlms_glc(e)','EX_tmacmp(e)','EX_tolcp(e)','EX_tolcp_ac(e)','EX_tolcp_ac_glc(e)','EX_tolcp_am(e)','EX_tolcp_am_glc(e)','EX_tolcp_glc(e)','EX_tpno_1glc_4g(e)','EX_tpno_4g(e)','EX_tpno_4glc(e)','EX_tpnoh(e)','EX_tsacmgluc(e)','EX_estroneglc(e)','EX_estrone(e)','EX_estradiolglc(e)','EX_estradiol(e)','EX_estriolglc(e)','EX_estriol(e)','EX_regfnb_glc(e)','EX_regfnb(e)','EX_glcur(e)'}
    {'1HIBUP_S_GLCAASE'},{'GLCURt2r'},{'GLCURt2r','EX_glcur(e)'}
    {'GALASE_LACTL'},{'LACTLt'}, {'EX_lactl(e)','LACTLt'}
    {'GALASE_LACTL'},{'GALt1r'}, {'EX_gal(e)','GALt1r'}
    {'GALASE_LACTL'},{'HEX7'}, {'HEX7'}
    {'DIHYDRO_DIGOXINc'},{'DIGOXINt2r'}, {'EX_digoxin(e)','EX_digitoxin(e)','EX_dihydro_digitoxin(e)','EX_dihydro_digoxin(e)','DIGOXINt2r','DIGOXINt2r','DIGITOXINt2r','DIHYDRO_DIGITOXINt2r','DIHYDRO_DIGOXINt2r'}
    {'PYNP_BRV'},{'BRVt2'},{'EX_brv(e)','EX_srv(e)','EX_bvu(e)','BRVt2','SRVt2','BVUte'}
    {'PYNP_BRV'},{'PPM'},{'NICRNS'}
    {'7AHSDH'},{'BIACt4'},{'BIACt4','EX_7ocholate(e)','BIACt1','EX_cholate(e)'}
    {'NADS1','NNDPR','QULNS'},{'NNATr'},{'NNATr'}
    {'TRPTA'},{'INDPYRD','INDRYPR','IOR'},{'EX_indpyr(e)','INDPYRt2r'}
    {'BTS4'},{'sink_s'},{'sink_s'}
    {'BTS4'},{'DM_btn'},{'DM_btn'}
    {'BTS4'},{'5DOAN'},{'DM_dad_5'}
    {'AMAOTr'},{'DM_AMOB'},{'DM_AMOB'}
    {'THZPSN'},{'DM_4HBA'},{'DM_4HBA'}
    {'DOPADH'},{'MTYMt2r'},{'MTYMt2r','EX_mtym(e)'}
    {'DOPADH'},{'3HLYTCL','DOPA34DHPHEt'},{'DOPAENT4tc','EX_dopa(e)'}
    {'3HLYTCL'},{'EX_dopa(e)','DOPADH'},{'EX_dopa(e)','DOPAt2'}
    {'3HLYTCL'},{'EX_34dhphe(e)'},{'EX_34dhphe(e)','34DHPHEt2'}
    {'3MOBS','MOHMT','DPRr','PANTS'},{'ASP1DC','AMAMTi'},{'ASP1DC'}
    {'ALKP_R788','GTPCII','DHNPA'},{'DNMPPA'},{'AKP1'}
    {'GTPCII','DHNPA','DHFS','HPPK','FOLD3'},{'AKP1'},{'DNMPPA','DNTPPA'}
    {'GTPCII2','DHPPDA2','APRAUR','RBFSa','RBFSb','RBFK'},{'PMDPHT'},{'PMDPHT'}
    {'AMAOTr'},{'AOXSr2'},{'AOXSr','CHCOAL','EX_pime(e)','PIMEtr'}
    {'PMACPME'},{'EX_meoh(e)'},{'EX_meoh(e)','MEOHt2'}
    {'PMACPME'},{'EACPR2'},{'EACPR2','3HACPR2','3OAACPR2','GACPCD','EACPR1','3HACPR1','3OAACPR1','MALCOACD','MALCOAMT'}
    {'DXYTST'},{'DM_this[c]'},{'sink_thissh[c]','DM_this[c]'}
    {'2IMZS'},{'EX_pcresol(e)'},{'EX_pcresol(e)','PCRESOLt2r'}
    {'EX_na1(e)'},{'DM_NA1'},{'DM_NA1'}
    {'IPMDr'},{'OMCDC'},{'OMCDC'}
    {'BAIZ1'},{'LCAT'},{'LCAT','DCAT','EX_dchac(e)','EX_HC02191(e)'}
    {'BAIZ1'},{'BIACt1'},{'BIACt1','BIACt2','BIACt3','EX_cholate(e)','EX_C02528(e)','EX_HC02194(e)'}
    {'ICCOAR2HICCOAT'},{'EX_isocapr(e)'},{'EX_isocapr(e)','ISOCAPRt2r'}
    {'IVCOASadp'},{'EX_isoval(e)'},{'EX_isoval(e)','ISOVALt2r'}
    {'INDRYPR'},{'EX_indlac(e)'},{'EX_indlac(e)','INDLACt'}
    {'INDPRPCOAINDLAACCOAT'},{'EX_ind3ppa(e)'},{'EX_ind3ppa(e)','IND3PPAt2r'}
    {'PHACK'},{'EX_pac(e)'},{'EX_pac(e)','PACt2r'}
    {'HPHACK'},{'EX_4hphac(e)'},{'EX_4hphac(e)','HPACt2r'}
    {'PPPNCOAPLACOAT'},{'EX_pppn(e)'},{'EX_pppn(e)','PPPNt2r'}
    {'4HPPCOA4HPLCOAT'},{'EX_r34hpp(e)'},{'EX_r34hpp(e)','4HPLt2r'}
    {'PYNP_BRV','PUNP1'},{'NICRNS'},{'EX_ade(e)','ADEt2r'}
    {'N2Ormq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'NO2rPmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'NO3rPmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'TMAOR1'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'TMAOR1e'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'DMSORmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'TTHrmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'TMAORmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'THSr1mq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'SELRmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'PSFrmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t','EX_ph2s(e)'}
    {'SUCDimq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'CYOmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'NO2rDmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'APSRmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'SO3rDmq'},{'EX_mqn8(e)'},{'EX_mqn8(e)','MK8t'}
    {'TMAOR2'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'TMAOR2e'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'THSr1dmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'SO3rDdmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'TTHrdmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'TMAORdmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'APSRdmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'SELRdmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'DMSORdmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc'}
    {'PSFrdmq'},{'EX_2dmmq8(e)'},{'EX_2dmmq8(e)','2DMMQ8abc','EX_ph2s(e)'}
    };

% Add reaction-specific gapfills to the organism-specific reaction sets
% where applicable
Orgs=unique(genomeAnnotation(:,1));
cnt=size(genomeAnnotation,1);
for i=1:length(Orgs)
    OrgRxns={};
    OrgRxnInds=[];
    OrgRxns(:,1)=genomeAnnotation(find(strcmp(Orgs{i},genomeAnnotation(:,1))),2);
    OrgRxns(:,2)=genomeAnnotation(find(strcmp(Orgs{i},genomeAnnotation(:,1))),3);
    OrgRxnInds(:,1)=find(strcmp(Orgs{i},genomeAnnotation(:,1)));
    for j=2:size(gapfills,1)
        if length(intersect(OrgRxns(:,1),gapfills{j,1}))==length(gapfills{j,1}) && isempty(intersect(OrgRxns(:,1),gapfills{j,2}))
            for k=1:length(gapfills{j,3})
            genomeAnnotation{cnt,1}=Orgs{i};
            genomeAnnotation{cnt,2}=gapfills{j,3}{k};
            genomeAnnotation{cnt,3}='gap_filled';
            cnt=cnt+1;
            end
        end
    end
end

% Delete reactions that will always be blocked

toDelete={
    'Present','Absent','DeleteRxns'
    {'1HIBUPGLU_St'},{'1HIBUP_S_GLCAASE','1HIBUP_S_GLCAASEe'},{'1HIBUPGLU_St','EX_1hibupglu_S(e)','1HMDGLUCt','EX_1hmdgluc(e)','2HATVACIDGLUCt','EX_2hatvacidgluc(e)','2HATVLACGLUCt','EX_2hatvlacgluc(e)','2HIBUPGLU_St','EX_2hibupglu_S(e)','2OH_CBZ_GLCt','EX_2oh_cbz_glc(e)','2OH_MTZ_GLCt','EX_2oh_mtz_glc(e)','3HIBUPGLU_St','EX_3hibupglu_S(e)','3OH_CBZ_GLCt','EX_3oh_cbz_glc(e)','3OH_DLOR_GLCt','EX_3oh_dlor_glc(e)','3OH_MDEA_GLCt','EX_3oh_mdea_glc(e)','3OH_MXN_GLCt','EX_3oh_mxn_glc(e)','4DH_TPNO_1GLCt','EX_4dh_tpno_1glc(e)','4HMDGLUCt','EX_4hmdgluc(e)','4OH_DCF_GLCt','EX_4oh_dcf_glc(e)','4OH_KP_GLCt','EX_4oh_kp_glc(e)','4OH_LEVOLE_GLCt','EX_4oh_levole_glc(e)','4OH_METH_GLCt','EX_4oh_meth_glc(e)','4OH_PROPL_GLCt','EX_4oh_propl_glc(e)','4OH_TRZ_GLCt','EX_4oh_trz_glc(e)','4OH_VCZ_GLCt','EX_4oh_vcz_glc(e)','5OH_SULFP_GLCt','EX_5oh_sulfp_glc(e)','5OHFVSGLUt','EX_5ohfvsglu(e)','6BHGLZGLCt','EX_6bhglzglc(e)','6OHFVSGLUt','EX_6ohfvsglu(e)','7BHGLZGLCt','EX_7bhglzglc(e)','7OH_EFV_GLCt','EX_7oh_efv_glc(e)','814DIOH_EFV_GLCt','EX_814dioh_efv_glc(e)','8OH_EFV_GLCt','EX_8oh_efv_glc(e)','AC_AMN_B_GLY_GLCt','EX_ac_amn_b_gly_glc(e)','ACMP_GLCt','EX_acmp_glc(e)','ACMPGLUt','EX_acmpglu(e)','ALPZ_4OH_GLCt','EX_alpz_4oh_glc(e)','ALPZ_AOH_GLCt','EX_alpz_aoh_glc(e)','AM14_GLCt','EX_am14_glc(e)','AM1CGLCt','EX_am1cglc(e)','AM5_GLCt','EX_am5_glc(e)','AM6_GLCt','EX_am6_glc(e)','AMIO_C_GLCt','EX_amio_c_glc(e)','AMIO_GLCt','EX_amio_glc(e)','AMN_B_GLY_GLCt','EX_amn_b_gly_glc(e)','AMNTD_M6_GLCt','EX_amntd_m6_glc(e)','ATVACYLGLUCt','EX_atvacylgluc(e)','ATVETHGLUCt','EX_atvethgluc(e)','ATVLACGLUCt','EX_atvlacgluc(e)','BHPM_GLCt','EX_bhpm_glc(e)','BILR_M10t','EX_bilr_M10(e)','BILR_M12t','EX_bilr_M12(e)','BILR_M15t','EX_bilr_M15(e)','BILR_M16t','EX_bilr_M16(e)','BSN_GLCt','EX_bsn_glc(e)','BZ_GLCt','EX_bz_glc(e)','CARIBUPGLU_St','EX_caribupglu_S(e)','CBZ_GLCt','EX_cbz_glc(e)','CD6168_GLCt','EX_cd6168_glc(e)','CHLPHNCL_GLCt','EX_chlphncl_glc(e)','CLCXB_C_GLCt','EX_clcxb_c_glc(e)','CLCXB_GLCt','EX_clcxb_glc(e)','CLOBI_GLCt','EX_clobi_glc(e)','CVM1GLUCt','EX_cvm1gluc(e)','CVM23GLUCt','EX_cvm23gluc(e)','DAA_GLCt','EX_daa_glc(e)','DCF_GLCt','EX_dcf_glc(e)','DDEA_GLCt','EX_ddea_glc(e)','DES_ASTZL_GLCt','EX_des_astzl_glc(e)','DIGOXIN_GLCt','EX_digoxin_glc(e)','DLB_GLCt','EX_dlb_glc(e)','DNPZ_M11t','EX_dnpz_m11(e)','DNPZ_M12t','EX_dnpz_m12(e)','DNPZ_M13t','EX_dnpz_m13(e)','DNPZ_M14t','EX_dnpz_m14(e)','DOH_ETR_GLCt','EX_doh_etr_glc(e)','DOH_VCZ_GLCt','EX_doh_vcz_glc(e)','DXO_GLCt','EX_dxo_glc(e)','EFV_GLCt','EX_efv_glc(e)','ELTR_GLCt','EX_eltr_glc(e)','ELTR_M3t','EX_eltr_m3(e)','ELTR_M4t','EX_eltr_m4(e)','EZTMB_GLCt','EX_eztmb_glc(e)','FVSGLUCt','EX_fvsgluc(e)','FVSTETGLUt','EX_fvstetglu(e)','GLC3MEACPt','EX_glc3meacp(e)','GLTMN_GLCt','EX_gltmn_glc(e)','GMFL_GLCt','EX_gmfl_glc(e)','GMFL_MI_GLCt','EX_gmfl_mI_glc(e)','GMFL_MII_GLCt','EX_gmfl_mII_glc(e)','GMFL_MIII_GLCt','EX_gmfl_mIII_glc(e)','GTACMPt','EX_gtacmp(e)','HST_3_GLCt','EX_hst_3_glc(e)','HST_37_DIGLCt','EX_hst_37_diglc(e)','HST_3GLC_7St','EX_hst_3glc_7s(e)','HST_7_GLCt','EX_hst_7_glc(e)','HST_7GLC_3St','EX_hst_7glc_3s(e)','IBUPGLUCt','EX_ibupgluc(e)','IMN_GLCt','EX_imn_glc(e)','INV_M1t','EX_inv_m1(e)','ISOSORBIDE_5MN_GLCt','EX_isosorbide_5mn_glc(e)','KPROFEN_GLCt','EX_kprofen_glc(e)','LSTN1GLUCt','EX_lstn1gluc(e)','LSTNM4t','EX_lstnm4(e)','LSTNM7t','EX_lstnm7(e)','MDZ_GLCt','EX_mdz_glc(e)','MDZGLCt','EX_mdzglc(e)','MISO_GLCt','EX_miso_glc(e)','MRPHN_3GLCt','EX_mrphn_3glc(e)','MRPHN_6GLCt','EX_mrphn_6glc(e)','MTZ_GLCt','EX_mtz_glc(e)','N_OH_PHTN_GLCt','EX_N_oh_phtn_glc(e)','NSLDP_M5_GLCt','EX_nsldp_m5_glc(e)','NVERP_GLCt','EX_nverp_glc(e)','ODSM_EGLTMN_GLCt','EX_odsm_egltmn_glc(e)','ODSM_GLTMN_GLCt','EX_odsm_gltmn_glc(e)','OH_ETR_GLCt','EX_oh_etr_glc(e)','OH_PBL_GLCt','EX_oh_pbl_glc(e)','PHPPA_GLCt','EX_phppa_glc(e)','PHTN_GLCt','EX_phtn_glc(e)','PROB_GLCt','EX_prob_glc(e)','PRONT_GLCt','EX_pront_glc(e)','PROPL_GLCt','EX_propl_glc(e)','PRX_MI_GLCt','EX_prx_mI_glc(e)','PRX_MII_GLCt','EX_prx_mII_glc(e)','PTVSTGLUCt','EX_ptvstgluc(e)','PVSGLUCt','EX_pvsgluc(e)','R_6OH_WARF_GLCt','EX_R_6oh_warf_glc(e)','R_7OH_WARF_GLCt','EX_R_7oh_warf_glc(e)','R_8OH_WARF_GLCt','EX_R_8oh_warf_glc(e)','R406_GLCt','EX_r406_glc(e)','R529_GLCt','EX_r529_glc(e)','REP_GLCt','EX_rep_glc(e)','RPN_104557_CB_GLCt','EX_rpn_104557_cb_glc(e)','RPN_96990_GLCt','EX_rpn_96990_glc(e)','RPN_OH_GLCt','EX_rpn_oh_glc(e)','RSVGLUCt','EX_rsvgluc(e)','S_4OH_WARF_GLCt','EX_S_4oh_warf_glc(e)','S_6OH_WARF_GLCt','EX_S_6oh_warf_glc(e)','SCH_488128t','EX_sch_488128(e)','SCH_57871_GLCt','EX_sch_57871_glc(e)','SFND_1689_GLCt','EX_sfnd_1689_glc(e)','SFTZ_GLCt','EX_sftz_glc(e)','SIMVGLUCt','EX_simvgluc(e)','SMAP_GLCt','EX_smap_glc(e)','SN38Gt','EX_sn38g(e)','SPZ_GLCt','EX_spz_glc(e)','SPZ_SFN_GLCt','EX_spz_sfn_glc(e)','STG_M3t','EX_stg_m3(e)','STG_M4t','EX_stg_m4(e)','TATt','EX_tat(e)','TGZ_GLCt','EX_tgz_glc(e)','TLF_A_M1t','EX_tlf_a_m1(e)','TLF_A_M2t','EX_tlf_a_m2(e)','TLF_A_M3t','EX_tlf_a_m3(e)','TLF_A_M4At','EX_tlf_a_m4a(e)','TLF_A_M4t','EX_tlf_a_m4(e)','TLF_A_M5At','EX_tlf_a_m5a(e)','TLF_A_M5Bt','EX_tlf_a_m5b(e)','TLF_A_M5t','EX_tlf_a_m5(e)','TLF_A_M6t','EX_tlf_a_m6(e)','TLF_A_M9t','EX_tlf_a_m9(e)','TLMS_GLCt','EX_tlms_glc(e)','TOLCP_AC_GLCt','EX_tolcp_ac_glc(e)','TOLCP_AM_GLCt','EX_tolcp_am_glc(e)','TOLCP_GLCt','EX_tolcp_glc(e)','TPNO_1GLC_4Gt','EX_tpno_1glc_4g(e)','TPNO_4GLCt','EX_tpno_4glc(e)','TSACMGLUCt','EX_tsacmgluc(e)'}
    {'1HIBUPGLU_St2'},{'1HIBUP_S_GLCAASE','1HIBUP_S_GLCAASEe'},{'1HIBUPGLU_St2','EX_1hibupglu_S(e)','1HMDGLUCt2','EX_1hmdgluc(e)','2HATVACIDGLUCt2','EX_2hatvacidgluc(e)','2HATVLACGLUCt2','EX_2hatvlacgluc(e)','2HIBUPGLU_St2','EX_2hibupglu_S(e)','2OH_CBZ_GLCt2','EX_2oh_cbz_glc(e)','2OH_MTZ_GLCt2','EX_2oh_mtz_glc(e)','3HIBUPGLU_St2','EX_3hibupglu_S(e)','3OH_CBZ_GLCt2','EX_3oh_cbz_glc(e)','3OH_DLOR_GLCt2','EX_3oh_dlor_glc(e)','3OH_MDEA_GLCt2','EX_3oh_mdea_glc(e)','3OH_MXN_GLCt2','EX_3oh_mxn_glc(e)','4DH_TPNO_1GLCt2','EX_4dh_tpno_1glc(e)','4HMDGLUCt2','EX_4hmdgluc(e)','4OH_DCF_GLCt2','EX_4oh_dcf_glc(e)','4OH_KP_GLCt2','EX_4oh_kp_glc(e)','4OH_LEVOLE_GLCt2','EX_4oh_levole_glc(e)','4OH_METH_GLCt2','EX_4oh_meth_glc(e)','4OH_PROPL_GLCt2','EX_4oh_propl_glc(e)','4OH_TRZ_GLCt2','EX_4oh_trz_glc(e)','4OH_VCZ_GLCt2','EX_4oh_vcz_glc(e)','5OH_SULFP_GLCt2','EX_5oh_sulfp_glc(e)','5OHFVSGLUt2','EX_5ohfvsglu(e)','6BHGLZGLCt2','EX_6bhglzglc(e)','6OHFVSGLUt2','EX_6ohfvsglu(e)','7BHGLZGLCt2','EX_7bhglzglc(e)','7OH_EFV_GLCt2','EX_7oh_efv_glc(e)','814DIOH_EFV_GLCt2','EX_814dioh_efv_glc(e)','8OH_EFV_GLCt2','EX_8oh_efv_glc(e)','AC_AMN_B_GLY_GLCt2','EX_ac_amn_b_gly_glc(e)','ACMP_GLCt2','EX_acmp_glc(e)','ACMPGLUt2','EX_acmpglu(e)','ALPZ_4OH_GLCt2','EX_alpz_4oh_glc(e)','ALPZ_AOH_GLCt2','EX_alpz_aoh_glc(e)','AM14_GLCt2','EX_am14_glc(e)','AM1CGLCt2','EX_am1cglc(e)','AM5_GLCt2','EX_am5_glc(e)','AM6_GLCt2','EX_am6_glc(e)','AMIO_C_GLCt2','EX_amio_c_glc(e)','AMIO_GLCt2','EX_amio_glc(e)','AMN_B_GLY_GLCt2','EX_amn_b_gly_glc(e)','AMNTD_M6_GLCt2','EX_amntd_m6_glc(e)','ATVACYLGLUCt2','EX_atvacylgluc(e)','ATVETHGLUCt2','EX_atvethgluc(e)','ATVLACGLUCt2','EX_atvlacgluc(e)','BHPM_GLCt2','EX_bhpm_glc(e)','BILR_M10t2','EX_bilr_M10(e)','BILR_M12t2','EX_bilr_M12(e)','BILR_M15t2','EX_bilr_M15(e)','BILR_M16t2','EX_bilr_M16(e)','BSN_GLCt2','EX_bsn_glc(e)','BZ_GLCt2','EX_bz_glc(e)','CARIBUPGLU_St2','EX_caribupglu_S(e)','CBZ_GLCt2','EX_cbz_glc(e)','CD6168_GLCt2','EX_cd6168_glc(e)','CHLPHNCL_GLCt2','EX_chlphncl_glc(e)','CLCXB_C_GLCt2','EX_clcxb_c_glc(e)','CLCXB_GLCt2','EX_clcxb_glc(e)','CLOBI_GLCt2','EX_clobi_glc(e)','CVM1GLUCt2','EX_cvm1gluc(e)','CVM23GLUCt2','EX_cvm23gluc(e)','DAA_GLCt2','EX_daa_glc(e)','DCF_GLCt2','EX_dcf_glc(e)','DDEA_GLCt2','EX_ddea_glc(e)','DES_ASTZL_GLCt2','EX_des_astzl_glc(e)','DIGOXIN_GLCt2','EX_digoxin_glc(e)','DLB_GLCt2','EX_dlb_glc(e)','DNPZ_M11t2','EX_dnpz_m11(e)','DNPZ_M12t2','EX_dnpz_m12(e)','DNPZ_M13t2','EX_dnpz_m13(e)','DNPZ_M14t2','EX_dnpz_m14(e)','DOH_ETR_GLCt2','EX_doh_etr_glc(e)','DOH_VCZ_GLCt2','EX_doh_vcz_glc(e)','DXO_GLCt2','EX_dxo_glc(e)','EFV_GLCt2','EX_efv_glc(e)','ELTR_GLCt2','EX_eltr_glc(e)','ELTR_M3t2','EX_eltr_m3(e)','ELTR_M4t2','EX_eltr_m4(e)','EZTMB_GLCt2','EX_eztmb_glc(e)','FVSGLUCt2','EX_fvsgluc(e)','FVSTETGLUt2','EX_fvstetglu(e)','GLC3MEACPt2','EX_glc3meacp(e)','GLTMN_GLCt2','EX_gltmn_glc(e)','GMFL_GLCt2','EX_gmfl_glc(e)','GMFL_MI_GLCt2','EX_gmfl_mI_glc(e)','GMFL_MII_GLCt2','EX_gmfl_mII_glc(e)','GMFL_MIII_GLCt2','EX_gmfl_mIII_glc(e)','GTACMPt2','EX_gtacmp(e)','HST_3_GLCt2','EX_hst_3_glc(e)','HST_37_DIGLCt2','EX_hst_37_diglc(e)','HST_3GLC_7St2','EX_hst_3glc_7s(e)','HST_7_GLCt2','EX_hst_7_glc(e)','HST_7GLC_3St2','EX_hst_7glc_3s(e)','IBUPGLUCt2','EX_ibupgluc(e)','IMN_GLCt2','EX_imn_glc(e)','INV_M1t2','EX_inv_m1(e)','ISOSORBIDE_5MN_GLCt2','EX_isosorbide_5mn_glc(e)','KPROFEN_GLCt2','EX_kprofen_glc(e)','LSTN1GLUCt2','EX_lstn1gluc(e)','LSTNM4t2','EX_lstnm4(e)','LSTNM7t2','EX_lstnm7(e)','MDZ_GLCt2','EX_mdz_glc(e)','MDZGLCt2','EX_mdzglc(e)','MISO_GLCt2','EX_miso_glc(e)','MRPHN_3GLCt2','EX_mrphn_3glc(e)','MRPHN_6GLCt2','EX_mrphn_6glc(e)','MTZ_GLCt2','EX_mtz_glc(e)','N_OH_PHTN_GLCt2','EX_N_oh_phtn_glc(e)','NSLDP_M5_GLCt2','EX_nsldp_m5_glc(e)','NVERP_GLCt2','EX_nverp_glc(e)','ODSM_EGLTMN_GLCt2','EX_odsm_egltmn_glc(e)','ODSM_GLTMN_GLCt2','EX_odsm_gltmn_glc(e)','OH_ETR_GLCt2','EX_oh_etr_glc(e)','OH_PBL_GLCt2','EX_oh_pbl_glc(e)','PHPPA_GLCt2','EX_phppa_glc(e)','PHTN_GLCt2','EX_phtn_glc(e)','PROB_GLCt2','EX_prob_glc(e)','PRONT_GLCt2','EX_pront_glc(e)','PROPL_GLCt2','EX_propl_glc(e)','PRX_MI_GLCt2','EX_prx_mI_glc(e)','PRX_MII_GLCt2','EX_prx_mII_glc(e)','PTVSTGLUCt2','EX_ptvstgluc(e)','PVSGLUCt2','EX_pvsgluc(e)','R_6OH_WARF_GLCt2','EX_R_6oh_warf_glc(e)','R_7OH_WARF_GLCt2','EX_R_7oh_warf_glc(e)','R_8OH_WARF_GLCt2','EX_R_8oh_warf_glc(e)','R406_GLCt2','EX_r406_glc(e)','R529_GLCt2','EX_r529_glc(e)','REP_GLCt2','EX_rep_glc(e)','RPN_104557_CB_GLCt2','EX_rpn_104557_cb_glc(e)','RPN_96990_GLCt2','EX_rpn_96990_glc(e)','RPN_OH_GLCt2','EX_rpn_oh_glc(e)','RSVGLUCt2','EX_rsvgluc(e)','S_4OH_WARF_GLCt2','EX_S_4oh_warf_glc(e)','S_6OH_WARF_GLCt2','EX_S_6oh_warf_glc(e)','SCH_488128t2','EX_sch_488128(e)','SCH_57871_GLCt2','EX_sch_57871_glc(e)','SFND_1689_GLCt2','EX_sfnd_1689_glc(e)','SFTZ_GLCt2','EX_sftz_glc(e)','SIMVGLUCt2','EX_simvgluc(e)','SMAP_GLCt2','EX_smap_glc(e)','SN38Gt2','EX_sn38g(e)','SPZ_GLCt2','EX_spz_glc(e)','SPZ_SFN_GLCt2','EX_spz_sfn_glc(e)','STG_M3t2','EX_stg_m3(e)','STG_M4t2','EX_stg_m4(e)','TATt2','EX_tat(e)','TGZ_GLCt2','EX_tgz_glc(e)','TLF_A_M1t2','EX_tlf_a_m1(e)','TLF_A_M2t2','EX_tlf_a_m2(e)','TLF_A_M3t2','EX_tlf_a_m3(e)','TLF_A_M4At2','EX_tlf_a_m4a(e)','TLF_A_M4t2','EX_tlf_a_m4(e)','TLF_A_M5At2','EX_tlf_a_m5a(e)','TLF_A_M5Bt2','EX_tlf_a_m5b(e)','TLF_A_M5t2','EX_tlf_a_m5(e)','TLF_A_M6t2','EX_tlf_a_m6(e)','TLF_A_M9t2','EX_tlf_a_m9(e)','TLMS_GLCt2','EX_tlms_glc(e)','TOLCP_AC_GLCt2','EX_tolcp_ac_glc(e)','TOLCP_AM_GLCt2','EX_tolcp_am_glc(e)','TOLCP_GLCt2','EX_tolcp_glc(e)','TPNO_1GLC_4Gt2','EX_tpno_1glc_4g(e)','TPNO_4GLCt2','EX_tpno_4glc(e)','TSACMGLUCt2','EX_tsacmgluc(e)'}
    };

Orgs=unique(genomeAnnotation(:,1));
delInd=[];
for i=1:length(Orgs)
    OrgRxns={};
    OrgRxnInds=[];
    OrgRxns(:,1)=genomeAnnotation(find(strcmp(Orgs{i},genomeAnnotation(:,1))),2);
    OrgRxns(:,2)=genomeAnnotation(find(strcmp(Orgs{i},genomeAnnotation(:,1))),3);
    OrgRxnInds(:,1)=find(strcmp(Orgs{i},genomeAnnotation(:,1)));
    for j=2:size(toDelete,1)
        if length(intersect(OrgRxns(:,1),toDelete{j,1}))==length(toDelete{j,1}) && isempty(intersect(OrgRxns(:,1),toDelete{j,2}))
            [C,IA]=intersect(OrgRxns(:,1),toDelete{j,3});
            delInd=horzcat(delInd,OrgRxnInds(IA,1));
        end
    end
end
genomeAnnotation(delInd,:)=[];

% manually add some pathways based on information from the literature
% Papers: PMIDs 11082195,30310076,30962433,29761785,31196984,32571913
manuallyAdded={'Olsenella_uli_DSM_7084','IND3ACDC','E1QXZ2';'Olsenella_uli_DSM_7084','IND3ACt2r','gap_filled';'Olsenella_uli_DSM_7084','EX_ind3ac(e)','exchange_reaction';'Olsenella_uli_DSM_7084','SKATOLEt2r','gap_filled';'Olsenella_uli_DSM_7084','EX_skatole(e)','exchange_reaction';'Olsenella_uli_DSM_7084','4HPHACDC','E1QVI8';'Olsenella_uli_DSM_7084','PCRESOLt2r','gap_filled';'Olsenella_uli_DSM_7084','EX_pcresol(e)','exchange_reaction';'Olsenella_uli_DSM_7084','HPACt2r','gap_filled';'Olsenella_uli_DSM_7084','EX_4hphac(e)','exchange_reaction';'Clostridium_botulinum_BKT015925','IND3ACDC','A0A0L7NFY0';'Clostridium_botulinum_BKT015925','IND3ACt2r','gap_filled';'Clostridium_botulinum_BKT015925','EX_ind3ac(e)','exchange_reaction';'Clostridium_botulinum_BKT015925','SKATOLEt2r','gap_filled';'Clostridium_botulinum_BKT015925','EX_skatole(e)','exchange_reaction';'Clostridium_botulinum_BKT015925','4HPHACDC','A0A0M1LIM4';'Clostridium_botulinum_BKT015925','HPACt2r','gap_filled';'Clostridium_botulinum_BKT015925','EX_4hphac(e)','exchange_reaction';'Clostridium_botulinum_C_str_Eklund','IND3ACDC','B1BA70';'Clostridium_botulinum_C_str_Eklund','IND3ACt2r','gap_filled';'Clostridium_botulinum_C_str_Eklund','EX_ind3ac(e)','exchange_reaction';'Clostridium_botulinum_C_str_Eklund','SKATOLEt2r','gap_filled';'Clostridium_botulinum_C_str_Eklund','EX_skatole(e)','exchange_reaction';'Bilophila_wadsworthia_ATCC_49260','ISETACSL','WP_005024906.1';'Bilophila_wadsworthia_3_1_6','ISETACSL','WP_005024906.1';'Desulfovibrio_piger_ATCC_29098','ISETACSL','B6WXM2';'Desulfovibrio_piger_ATCC_29098','ISETACt2r','gap_filled';'Desulfovibrio_piger_ATCC_29098','EX_isetac(e)','exchange_reaction';'Desulfovibrio_desulfuricans_subsp_desulfuricans_DSM_642','ISETACSL','WP_022659977.1';'Desulfovibrio_desulfuricans_subsp_desulfuricans_DSM_642','ISETACt2r','gap_filled';'Desulfovibrio_desulfuricans_subsp_desulfuricans_DSM_642','EX_isetac(e)','exchange_reaction';'Eggerthella_lenta_11C','DIGITOXINt2r','gap_filled';'Eggerthella_lenta_11C','DIGOXINt2r','gap_filled';'Eggerthella_lenta_11C','DIHYDRO_DIGITOXINc','cgr2';'Eggerthella_lenta_11C','DIHYDRO_DIGITOXINt2r','gap_filled';'Eggerthella_lenta_11C','DIHYDRO_DIGOXINc','cgr2';'Eggerthella_lenta_11C','DIHYDRO_DIGOXINt2r','gap_filled';'Eggerthella_lenta_11C','EX_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_11C','EX_digoxin(e)','exchange_reaction';'Eggerthella_lenta_11C','EX_dihydro_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_11C','EX_dihydro_digoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11767','DIGITOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11767','DIGOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11767','DIHYDRO_DIGITOXINc','cgr2';'Eggerthella_lenta_DSM_11767','DIHYDRO_DIGITOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11767','DIHYDRO_DIGOXINc','cgr2';'Eggerthella_lenta_DSM_11767','DIHYDRO_DIGOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11767','EX_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11767','EX_digoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11767','EX_dihydro_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11767','EX_dihydro_digoxin(e)','exchange_reaction';'Eggerthella_lenta_CC86D54','DIGITOXINt2r','gap_filled';'Eggerthella_lenta_CC86D54','DIGOXINt2r','gap_filled';'Eggerthella_lenta_CC86D54','DIHYDRO_DIGITOXINc','cgr2';'Eggerthella_lenta_CC86D54','DIHYDRO_DIGITOXINt2r','gap_filled';'Eggerthella_lenta_CC86D54','DIHYDRO_DIGOXINc','cgr2';'Eggerthella_lenta_CC86D54','DIHYDRO_DIGOXINt2r','gap_filled';'Eggerthella_lenta_CC86D54','EX_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_CC86D54','EX_digoxin(e)','exchange_reaction';'Eggerthella_lenta_CC86D54','EX_dihydro_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_CC86D54','EX_dihydro_digoxin(e)','exchange_reaction';'Eggerthella_lenta_AB12n2','DIGITOXINt2r','gap_filled';'Eggerthella_lenta_AB12n2','DIGOXINt2r','gap_filled';'Eggerthella_lenta_AB12n2','DIHYDRO_DIGITOXINc','cgr2';'Eggerthella_lenta_AB12n2','DIHYDRO_DIGITOXINt2r','gap_filled';'Eggerthella_lenta_AB12n2','DIHYDRO_DIGOXINc','cgr2';'Eggerthella_lenta_AB12n2','DIHYDRO_DIGOXINt2r','gap_filled';'Eggerthella_lenta_AB12n2','EX_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_AB12n2','EX_digoxin(e)','exchange_reaction';'Eggerthella_lenta_AB12n2','EX_dihydro_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_AB12n2','EX_dihydro_digoxin(e)','exchange_reaction';'Eggerthella_lenta_AB8n2','DIGITOXINt2r','gap_filled';'Eggerthella_lenta_AB8n2','DIGOXINt2r','gap_filled';'Eggerthella_lenta_AB8n2','DIHYDRO_DIGITOXINc','cgr2';'Eggerthella_lenta_AB8n2','DIHYDRO_DIGITOXINt2r','gap_filled';'Eggerthella_lenta_AB8n2','DIHYDRO_DIGOXINc','cgr2';'Eggerthella_lenta_AB8n2','DIHYDRO_DIGOXINt2r','gap_filled';'Eggerthella_lenta_AB8n2','EX_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_AB8n2','EX_digoxin(e)','exchange_reaction';'Eggerthella_lenta_AB8n2','EX_dihydro_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_AB8n2','EX_dihydro_digoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11863','DIGITOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11863','DIGOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11863','DIHYDRO_DIGITOXINc','cgr2';'Eggerthella_lenta_DSM_11863','DIHYDRO_DIGITOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11863','DIHYDRO_DIGOXINc','cgr2';'Eggerthella_lenta_DSM_11863','DIHYDRO_DIGOXINt2r','gap_filled';'Eggerthella_lenta_DSM_11863','EX_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11863','EX_digoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11863','EX_dihydro_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_DSM_11863','EX_dihydro_digoxin(e)','exchange_reaction';'Eggerthella_lenta_326I6NA','DIGITOXINt2r','gap_filled';'Eggerthella_lenta_326I6NA','DIGOXINt2r','gap_filled';'Eggerthella_lenta_326I6NA','DIHYDRO_DIGITOXINc','cgr2';'Eggerthella_lenta_326I6NA','DIHYDRO_DIGITOXINt2r','gap_filled';'Eggerthella_lenta_326I6NA','DIHYDRO_DIGOXINc','cgr2';'Eggerthella_lenta_326I6NA','DIHYDRO_DIGOXINt2r','gap_filled';'Eggerthella_lenta_326I6NA','EX_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_326I6NA','EX_digoxin(e)','exchange_reaction';'Eggerthella_lenta_326I6NA','EX_dihydro_digitoxin(e)','exchange_reaction';'Eggerthella_lenta_326I6NA','EX_dihydro_digoxin(e)','exchange_reaction';'Bilophila_wadsworthia_3_1_6','EX_h2s(e)','gap_filled';'Bilophila_wadsworthia_3_1_6','H2St','gap_filled';'Bilophila_wadsworthia_3_1_6','EX_h2(e)','gap_filled';'Bilophila_wadsworthia_3_1_6','EX_for(e)','gap_filled';'Bilophila_wadsworthia_3_1_6','H2St','gap_filled';'Bilophila_wadsworthia_3_1_6','H2td','gap_filled';'Bilophila_wadsworthia_3_1_6','FORt','gap_filled';'Bilophila_wadsworthia_3_1_6','EX_pyr(e)','gap_filled';'Bilophila_wadsworthia_3_1_6','PYRt2r','gap_filled';'Bilophila_wadsworthia_3_1_6','SULR','gap_filled';'Bilophila_wadsworthia_3_1_6','TAURPYRAT','gap_filled';'Bilophila_wadsworthia_3_1_6','SACALDACT','gap_filled';'Bilophila_wadsworthia_ATCC_49260','EX_h2s(e)','gap_filled';'Bilophila_wadsworthia_ATCC_49260','H2St','gap_filled';'Bilophila_wadsworthia_ATCC_49260','EX_h2(e)','gap_filled';'Bilophila_wadsworthia_ATCC_49260','EX_for(e)','gap_filled';'Bilophila_wadsworthia_ATCC_49260','H2St','gap_filled';'Bilophila_wadsworthia_ATCC_49260','H2td','gap_filled';'Bilophila_wadsworthia_ATCC_49260','FORt','gap_filled';'Bilophila_wadsworthia_ATCC_49260','EX_pyr(e)','gap_filled';'Bilophila_wadsworthia_ATCC_49260','PYRt2r','gap_filled';'Bilophila_wadsworthia_ATCC_49260','SULR','gap_filled';'Bilophila_wadsworthia_ATCC_49260','TAURPYRAT','gap_filled';'Bilophila_wadsworthia_ATCC_49260','SACALDACT','gap_filled';'Eggerthella_lenta_1160AFAA','DOPADH','Dadh';'Eggerthella_lenta_1160AFAA','EX_dopa(e)','gap_filled';'Eggerthella_lenta_1160AFAA','DOPAENT4tc','gap_filled';'Eggerthella_lenta_1160AFAA','EX_mtym(e)','gap_filled';'Eggerthella_lenta_1160AFAA','MTYMt2r','gap_filled';'Eggerthella_lenta_11C','DOPADH','Dadh';'Eggerthella_lenta_11C','EX_dopa(e)','gap_filled';'Eggerthella_lenta_11C','DOPAENT4tc','gap_filled';'Eggerthella_lenta_11C','EX_mtym(e)','gap_filled';'Eggerthella_lenta_11C','MTYMt2r','gap_filled';'Eggerthella_lenta_14A','DOPADH','Dadh';'Eggerthella_lenta_14A','EX_dopa(e)','gap_filled';'Eggerthella_lenta_14A','DOPAENT4tc','gap_filled';'Eggerthella_lenta_14A','EX_mtym(e)','gap_filled';'Eggerthella_lenta_14A','MTYMt2r','gap_filled';'Eggerthella_lenta_28B','DOPADH','Dadh';'Eggerthella_lenta_28B','EX_dopa(e)','gap_filled';'Eggerthella_lenta_28B','DOPAENT4tc','gap_filled';'Eggerthella_lenta_28B','EX_mtym(e)','gap_filled';'Eggerthella_lenta_28B','MTYMt2r','gap_filled';'Eggerthella_lenta_326I6NA','DOPADH','Dadh';'Eggerthella_lenta_326I6NA','EX_dopa(e)','gap_filled';'Eggerthella_lenta_326I6NA','DOPAENT4tc','gap_filled';'Eggerthella_lenta_326I6NA','EX_mtym(e)','gap_filled';'Eggerthella_lenta_326I6NA','MTYMt2r','gap_filled';'Eggerthella_lenta_A2','DOPADH','Dadh';'Eggerthella_lenta_A2','EX_dopa(e)','gap_filled';'Eggerthella_lenta_A2','DOPAENT4tc','gap_filled';'Eggerthella_lenta_A2','EX_mtym(e)','gap_filled';'Eggerthella_lenta_A2','MTYMt2r','gap_filled';'Eggerthella_lenta_AB12n2','DOPADH','Dadh';'Eggerthella_lenta_AB12n2','EX_dopa(e)','gap_filled';'Eggerthella_lenta_AB12n2','DOPAENT4tc','gap_filled';'Eggerthella_lenta_AB12n2','EX_mtym(e)','gap_filled';'Eggerthella_lenta_AB12n2','MTYMt2r','gap_filled';'Eggerthella_lenta_AB8n2','DOPADH','Dadh';'Eggerthella_lenta_AB8n2','EX_dopa(e)','gap_filled';'Eggerthella_lenta_AB8n2','DOPAENT4tc','gap_filled';'Eggerthella_lenta_AB8n2','EX_mtym(e)','gap_filled';'Eggerthella_lenta_AB8n2','MTYMt2r','gap_filled';'Eggerthella_lenta_CC75D52','DOPADH','Dadh';'Eggerthella_lenta_CC75D52','EX_dopa(e)','gap_filled';'Eggerthella_lenta_CC75D52','DOPAENT4tc','gap_filled';'Eggerthella_lenta_CC75D52','EX_mtym(e)','gap_filled';'Eggerthella_lenta_CC75D52','MTYMt2r','gap_filled';'Eggerthella_lenta_CC82BHI2','DOPADH','Dadh';'Eggerthella_lenta_CC82BHI2','EX_dopa(e)','gap_filled';'Eggerthella_lenta_CC82BHI2','DOPAENT4tc','gap_filled';'Eggerthella_lenta_CC82BHI2','EX_mtym(e)','gap_filled';'Eggerthella_lenta_CC82BHI2','MTYMt2r','gap_filled';'Eggerthella_lenta_DSM_11767','DOPADH','Dadh';'Eggerthella_lenta_DSM_11767','EX_dopa(e)','gap_filled';'Eggerthella_lenta_DSM_11767','DOPAENT4tc','gap_filled';'Eggerthella_lenta_DSM_11767','EX_mtym(e)','gap_filled';'Eggerthella_lenta_DSM_11767','MTYMt2r','gap_filled';'Eggerthella_lenta_DSM_15644','DOPADH','Dadh';'Eggerthella_lenta_DSM_15644','EX_dopa(e)','gap_filled';'Eggerthella_lenta_DSM_15644','DOPAENT4tc','gap_filled';'Eggerthella_lenta_DSM_15644','EX_mtym(e)','gap_filled';'Eggerthella_lenta_DSM_15644','MTYMt2r','gap_filled';'Eggerthella_lenta_Valencia','DOPADH','Dadh';'Eggerthella_lenta_Valencia','EX_dopa(e)','gap_filled';'Eggerthella_lenta_Valencia','DOPAENT4tc','gap_filled';'Eggerthella_lenta_Valencia','EX_mtym(e)','gap_filled';'Eggerthella_lenta_Valencia','MTYMt2r','gap_filled';'Eggerthella_sinensis_DSM_16107','DOPADH','Dadh';'Eggerthella_sinensis_DSM_16107','EX_dopa(e)','gap_filled';'Eggerthella_sinensis_DSM_16107','DOPAENT4tc','gap_filled';'Eggerthella_sinensis_DSM_16107','EX_mtym(e)','gap_filled';'Eggerthella_sinensis_DSM_16107','MTYMt2r','gap_filled';'Paraeggerthella_hongkongensis_RC2_2','DOPADH','Dadh';'Paraeggerthella_hongkongensis_RC2_2','EX_dopa(e)','gap_filled';'Paraeggerthella_hongkongensis_RC2_2','DOPAENT4tc','gap_filled';'Paraeggerthella_hongkongensis_RC2_2','EX_mtym(e)','gap_filled';'Paraeggerthella_hongkongensis_RC2_2','MTYMt2r','gap_filled';'Bacteroides_fragilis_BOB25','BZD_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_BOB25','NEOPRONT_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_BOB25','OLSA_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_BOB25','PRONT_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_BOB25','SSZ_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_BOB25','BZD_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_BOB25','NEOPRONT_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_BOB25','OLSA_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_BOB25','PRONT_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_BOB25','SSZ_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_BOB25','5ASAt2r','gap_filled';'Bacteroides_fragilis_BOB25','ABZ_ALA_Bt2r','gap_filled';'Bacteroides_fragilis_BOB25','BZDt2r','gap_filled';'Bacteroides_fragilis_BOB25','NEOPRONTt2r','gap_filled';'Bacteroides_fragilis_BOB25','OLSAt2r','gap_filled';'Bacteroides_fragilis_BOB25','PRONTt2r','gap_filled';'Bacteroides_fragilis_BOB25','SANILAMIDEt2r','gap_filled';'Bacteroides_fragilis_BOB25','SSZt2r','gap_filled';'Bacteroides_fragilis_BOB25','SULFPt2r','gap_filled';'Bacteroides_fragilis_BOB25','TABt2r','gap_filled';'Bacteroides_fragilis_BOB25','EX_5asa(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_abz_ala_b(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_bzd(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_olsa(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_neopront(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_pront(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_sanilamide(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_ssz(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_sulfp(e)','gap_filled';'Bacteroides_fragilis_BOB25','EX_tab(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','BZD_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','NEOPRONT_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','OLSA_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','PRONT_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','SSZ_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','BZD_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','NEOPRONT_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','OLSA_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','PRONT_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','SSZ_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_NCTC_9343','5ASAt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','ABZ_ALA_Bt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','BZDt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','NEOPRONTt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','OLSAt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','PRONTt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','SANILAMIDEt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','SSZt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','SULFPt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','TABt2r','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_5asa(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_abz_ala_b(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_bzd(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_olsa(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_neopront(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_pront(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_sanilamide(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_ssz(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_sulfp(e)','gap_filled';'Bacteroides_fragilis_NCTC_9343','EX_tab(e)','gap_filled';'Bacteroides_fragilis_YCH46','BZD_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_YCH46','NEOPRONT_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_YCH46','OLSA_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_YCH46','PRONT_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_YCH46','SSZ_AR_NAD','AzoC_Cp';'Bacteroides_fragilis_YCH46','BZD_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_YCH46','NEOPRONT_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_YCH46','OLSA_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_YCH46','PRONT_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_YCH46','SSZ_AR_NADP','AzoC_Cp';'Bacteroides_fragilis_YCH46','5ASAt2r','gap_filled';'Bacteroides_fragilis_YCH46','ABZ_ALA_Bt2r','gap_filled';'Bacteroides_fragilis_YCH46','BZDt2r','gap_filled';'Bacteroides_fragilis_YCH46','NEOPRONTt2r','gap_filled';'Bacteroides_fragilis_YCH46','OLSAt2r','gap_filled';'Bacteroides_fragilis_YCH46','PRONTt2r','gap_filled';'Bacteroides_fragilis_YCH46','SANILAMIDEt2r','gap_filled';'Bacteroides_fragilis_YCH46','SSZt2r','gap_filled';'Bacteroides_fragilis_YCH46','SULFPt2r','gap_filled';'Bacteroides_fragilis_YCH46','TABt2r','gap_filled';'Bacteroides_fragilis_YCH46','EX_5asa(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_abz_ala_b(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_bzd(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_olsa(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_neopront(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_pront(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_sanilamide(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_ssz(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_sulfp(e)','gap_filled';'Bacteroides_fragilis_YCH46','EX_tab(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','BZD_AR_NAD','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','NEOPRONT_AR_NAD','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','OLSA_AR_NAD','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','PRONT_AR_NAD','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','SSZ_AR_NAD','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','BZD_AR_NADP','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','NEOPRONT_AR_NADP','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','OLSA_AR_NADP','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','PRONT_AR_NADP','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','SSZ_AR_NADP','AzoC_Cp';'Bacteroides_ovatus_ATCC_8483','5ASAt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','ABZ_ALA_Bt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','BZDt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','NEOPRONTt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','OLSAt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','PRONTt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','SANILAMIDEt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','SSZt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','SULFPt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','TABt2r','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_5asa(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_abz_ala_b(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_bzd(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_olsa(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_neopront(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_pront(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_sanilamide(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_ssz(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_sulfp(e)','gap_filled';'Bacteroides_ovatus_ATCC_8483','EX_tab(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','BZD_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','NEOPRONT_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','OLSA_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','PRONT_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','SSZ_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','BZD_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','NEOPRONT_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','OLSA_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','PRONT_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','SSZ_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_ATCC_8482','5ASAt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','ABZ_ALA_Bt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','BZDt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','NEOPRONTt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','OLSAt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','PRONTt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','SANILAMIDEt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','SSZt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','SULFPt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','TABt2r','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_5asa(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_abz_ala_b(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_bzd(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_olsa(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_neopront(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_pront(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_sanilamide(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_ssz(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_sulfp(e)','gap_filled';'Bacteroides_vulgatus_ATCC_8482','EX_tab(e)','gap_filled';'Bacteroides_vulgatus_mpk','BZD_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_mpk','NEOPRONT_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_mpk','OLSA_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_mpk','PRONT_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_mpk','SSZ_AR_NAD','AzoC_Cp';'Bacteroides_vulgatus_mpk','BZD_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_mpk','NEOPRONT_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_mpk','OLSA_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_mpk','PRONT_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_mpk','SSZ_AR_NADP','AzoC_Cp';'Bacteroides_vulgatus_mpk','5ASAt2r','gap_filled';'Bacteroides_vulgatus_mpk','ABZ_ALA_Bt2r','gap_filled';'Bacteroides_vulgatus_mpk','BZDt2r','gap_filled';'Bacteroides_vulgatus_mpk','NEOPRONTt2r','gap_filled';'Bacteroides_vulgatus_mpk','OLSAt2r','gap_filled';'Bacteroides_vulgatus_mpk','PRONTt2r','gap_filled';'Bacteroides_vulgatus_mpk','SANILAMIDEt2r','gap_filled';'Bacteroides_vulgatus_mpk','SSZt2r','gap_filled';'Bacteroides_vulgatus_mpk','SULFPt2r','gap_filled';'Bacteroides_vulgatus_mpk','TABt2r','gap_filled';'Bacteroides_vulgatus_mpk','EX_5asa(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_abz_ala_b(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_bzd(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_olsa(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_neopront(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_pront(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_sanilamide(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_ssz(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_sulfp(e)','gap_filled';'Bacteroides_vulgatus_mpk','EX_tab(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','BZD_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','NEOPRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','OLSA_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','PRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','SSZ_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','BZD_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','NEOPRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','OLSA_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','PRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','SSZ_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_BGN4','5ASAt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','ABZ_ALA_Bt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','BZDt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','NEOPRONTt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','OLSAt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','PRONTt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','SANILAMIDEt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','SSZt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','SULFPt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','TABt2r','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_5asa(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_abz_ala_b(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_bzd(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_olsa(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_neopront(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_pront(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_sanilamide(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_ssz(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_sulfp(e)','gap_filled';'Bifidobacterium_bifidum_BGN4','EX_tab(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','BZD_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','NEOPRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','OLSA_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','PRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','SSZ_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','BZD_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','NEOPRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','OLSA_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','PRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','SSZ_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_LMG_13195','5ASAt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','ABZ_ALA_Bt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','BZDt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','NEOPRONTt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','OLSAt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','PRONTt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','SANILAMIDEt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','SSZt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','SULFPt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','TABt2r','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_5asa(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_abz_ala_b(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_bzd(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_olsa(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_neopront(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_pront(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_sanilamide(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_ssz(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_sulfp(e)','gap_filled';'Bifidobacterium_bifidum_LMG_13195','EX_tab(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','BZD_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','NEOPRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','OLSA_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','PRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','SSZ_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','BZD_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','NEOPRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','OLSA_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','PRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','SSZ_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_PRL2010','5ASAt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','ABZ_ALA_Bt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','BZDt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','NEOPRONTt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','OLSAt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','PRONTt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','SANILAMIDEt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','SSZt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','SULFPt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','TABt2r','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_5asa(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_abz_ala_b(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_bzd(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_olsa(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_neopront(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_pront(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_sanilamide(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_ssz(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_sulfp(e)','gap_filled';'Bifidobacterium_bifidum_PRL2010','EX_tab(e)','gap_filled';'Bifidobacterium_bifidum_S17','BZD_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_S17','NEOPRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_S17','OLSA_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_S17','PRONT_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_S17','SSZ_AR_NAD','AzoR_Ec';'Bifidobacterium_bifidum_S17','BZD_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_S17','NEOPRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_S17','OLSA_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_S17','PRONT_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_S17','SSZ_AR_NADP','AzoR_Ec';'Bifidobacterium_bifidum_S17','5ASAt2r','gap_filled';'Bifidobacterium_bifidum_S17','ABZ_ALA_Bt2r','gap_filled';'Bifidobacterium_bifidum_S17','BZDt2r','gap_filled';'Bifidobacterium_bifidum_S17','NEOPRONTt2r','gap_filled';'Bifidobacterium_bifidum_S17','OLSAt2r','gap_filled';'Bifidobacterium_bifidum_S17','PRONTt2r','gap_filled';'Bifidobacterium_bifidum_S17','SANILAMIDEt2r','gap_filled';'Bifidobacterium_bifidum_S17','SSZt2r','gap_filled';'Bifidobacterium_bifidum_S17','SULFPt2r','gap_filled';'Bifidobacterium_bifidum_S17','TABt2r','gap_filled';'Bifidobacterium_bifidum_S17','EX_5asa(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_abz_ala_b(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_bzd(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_olsa(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_neopront(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_pront(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_sanilamide(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_ssz(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_sulfp(e)','gap_filled';'Bifidobacterium_bifidum_S17','EX_tab(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','BZD_AR_NAD','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','NEOPRONT_AR_NAD','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','OLSA_AR_NAD','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','PRONT_AR_NAD','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','SSZ_AR_NAD','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','BZD_AR_NADP','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','NEOPRONT_AR_NADP','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','OLSA_AR_NADP','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','PRONT_AR_NADP','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','SSZ_AR_NADP','AGH15624.1';'Clostridium_perfringens_B_str_ATCC_3626','5ASAt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','ABZ_ALA_Bt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','BZDt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','NEOPRONTt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','OLSAt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','PRONTt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','SANILAMIDEt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','SSZt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','SULFPt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','TABt2r','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_5asa(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_abz_ala_b(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_bzd(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_olsa(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_neopront(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_pront(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_sanilamide(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_ssz(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_sulfp(e)','gap_filled';'Clostridium_perfringens_B_str_ATCC_3626','EX_tab(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','BZD_AR_NAD','AY422207.1';'Enterococcus_faecalis_ATCC_19433','NEOPRONT_AR_NAD','AY422207.1';'Enterococcus_faecalis_ATCC_19433','OLSA_AR_NAD','AY422207.1';'Enterococcus_faecalis_ATCC_19433','PRONT_AR_NAD','AY422207.1';'Enterococcus_faecalis_ATCC_19433','SSZ_AR_NAD','AY422207.1';'Enterococcus_faecalis_ATCC_19433','BZD_AR_NADP','AY422207.1';'Enterococcus_faecalis_ATCC_19433','NEOPRONT_AR_NADP','AY422207.1';'Enterococcus_faecalis_ATCC_19433','OLSA_AR_NADP','AY422207.1';'Enterococcus_faecalis_ATCC_19433','PRONT_AR_NADP','AY422207.1';'Enterococcus_faecalis_ATCC_19433','SSZ_AR_NADP','AY422207.1';'Enterococcus_faecalis_ATCC_19433','5ASAt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','ABZ_ALA_Bt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','BZDt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','NEOPRONTt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','OLSAt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','PRONTt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','SANILAMIDEt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','SSZt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','SULFPt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','TABt2r','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_5asa(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_abz_ala_b(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_bzd(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_olsa(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_neopront(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_pront(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_sanilamide(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_ssz(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_sulfp(e)','gap_filled';'Enterococcus_faecalis_ATCC_19433','EX_tab(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','BZD_AR_NAD','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','NEOPRONT_AR_NAD','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','OLSA_AR_NAD','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','PRONT_AR_NAD','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','SSZ_AR_NAD','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','BZD_AR_NADP','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','NEOPRONT_AR_NADP','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','OLSA_AR_NADP','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','PRONT_AR_NADP','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','SSZ_AR_NADP','NP_415930.1';'Escherichia_coli_str_K_12_substr_MG1655','5ASAt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','ABZ_ALA_Bt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','BZDt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','NEOPRONTt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','OLSAt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','PRONTt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','SANILAMIDEt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','SSZt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','SULFPt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','TABt2r','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_5asa(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_abz_ala_b(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_bzd(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_olsa(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_neopront(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_pront(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_sanilamide(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_ssz(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_sulfp(e)','gap_filled';'Escherichia_coli_str_K_12_substr_MG1655','EX_tab(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','BZD_AR_NAD','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','NEOPRONT_AR_NAD','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','OLSA_AR_NAD','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','PRONT_AR_NAD','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','SSZ_AR_NAD','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','BZD_AR_NADP','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','NEOPRONT_AR_NADP','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','OLSA_AR_NADP','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','PRONT_AR_NADP','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','SSZ_AR_NADP','AzoC_Cp or AzoEf1_Ef';'Odoribacter_splanchnicus_1651_6_DSM_20712','5ASAt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','ABZ_ALA_Bt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','BZDt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','NEOPRONTt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','OLSAt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','PRONTt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','SANILAMIDEt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','SSZt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','SULFPt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','TABt2r','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_5asa(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_abz_ala_b(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_bzd(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_olsa(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_neopront(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_pront(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_sanilamide(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_ssz(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_sulfp(e)','gap_filled';'Odoribacter_splanchnicus_1651_6_DSM_20712','EX_tab(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','BZD_AR_NAD','AAG04174';'Pseudomonas_aeruginosa_PAO1','NEOPRONT_AR_NAD','AAG04174';'Pseudomonas_aeruginosa_PAO1','OLSA_AR_NAD','AAG04174';'Pseudomonas_aeruginosa_PAO1','PRONT_AR_NAD','AAG04174';'Pseudomonas_aeruginosa_PAO1','SSZ_AR_NAD','AAG04174';'Pseudomonas_aeruginosa_PAO1','BZD_AR_NADP','AAG04174';'Pseudomonas_aeruginosa_PAO1','NEOPRONT_AR_NADP','AAG04174';'Pseudomonas_aeruginosa_PAO1','OLSA_AR_NADP','AAG04174';'Pseudomonas_aeruginosa_PAO1','PRONT_AR_NADP','AAG04174';'Pseudomonas_aeruginosa_PAO1','SSZ_AR_NADP','AAG04174';'Pseudomonas_aeruginosa_PAO1','5ASAt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','ABZ_ALA_Bt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','BZDt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','NEOPRONTt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','OLSAt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','PRONTt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','SANILAMIDEt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','SSZt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','SULFPt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','TABt2r','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_5asa(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_abz_ala_b(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_bzd(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_olsa(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_neopront(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_pront(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_sanilamide(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_ssz(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_sulfp(e)','gap_filled';'Pseudomonas_aeruginosa_PAO1','EX_tab(e)','gap_filled'};

genomeAnnotation=vertcat(genomeAnnotation,manuallyAdded);

% fix nomenclature
genomeAnnotation(:,3)=strrep(genomeAnnotation(:,3),'fig|','');
genomeAnnotation(:,3)=strrep(genomeAnnotation(:,3),'( ','(');
genomeAnnotation(:,3)=strrep(genomeAnnotation(:,3),' )',')');
genomeAnnotation(:,3)=strrep(genomeAnnotation(:,3),'OR','or');
genomeAnnotation(:,3)=strrep(genomeAnnotation(:,3),'AND','and');
genomeAnnotation(:,3)=strrep(genomeAnnotation(:,3),'  ',' or ');

gapfilledGenomeAnnotation=genomeAnnotation;

end
